Objective To compare the effects of ouabain and digoxin on the gene expression of sodium pump α-subunit isoforms in the myocardium of rats. Methods Normal Sprague-Dawley (SD) rats were injected with ouabain (20 μg· kg-1· d-1, i.p. ), digoxin (32 μg· kg-1· d-1, i.p. ) and normal saline (NS) once a day, respectively, and indirect systolic blood pressure was recorded once a week. Six weeks later, all of the rats were killed, and sodium pump α1-, α2-, and α3-subunit mRNA levels in the myocardium were detected with the reverse transcription polymerase chain reaction (RT-PCR) method. Results The systolic blood pressure of the rats infused with ouabain increased significantly at the end of week 6 ( 132.6 ± 9.0 mm Hg vs 115.7 ± 8.2 mm Hg, P ＜ 0.01 ), while no difference in blood pressure was found between the digoxin group and the NS group. The expression of sodium pump α-subunit isoforms in the ventricular myocardium was regulated by either ouabain or digoxin. Both ouabain and digoxin stimulated expression of the α3-isoform, whereas o2 was uncharcged in those two groups. α1-isoform expression decreased in the ouabain group and was unchanged in the digoxin group. Conclusions These results suggest that both ouabain and digoxin could regulate sodium pump α-subunit isoform expression, which might be related to the physiological roles of endogenous ouabain and might be responsible for the difference in the pharmacological and toxicological effects of ouabain and digoxin, including their effects on blood pressure.